7PSE

Crystal Structure of a Class D Carbapenemase_K73ALY Complexed with Oxacillin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4S2P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties
Matthews coefficientSolvent content
2.4449.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.83α = 90
b = 105.48β = 90
c = 124.96γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976270DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3253.7699.30.996710.926329
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.322.40.5661

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4S2P2.3253.7626280126699.2150.2380.23520.288646.938
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
4.801-0.452-4.349
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.754
r_dihedral_angle_3_deg16.295
r_dihedral_angle_4_deg14.331
r_lrange_it8.528
r_lrange_other8.528
r_dihedral_angle_1_deg7.153
r_mcangle_it6.128
r_mcangle_other6.128
r_scangle_it5.765
r_scangle_other5.764
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.754
r_dihedral_angle_3_deg16.295
r_dihedral_angle_4_deg14.331
r_lrange_it8.528
r_lrange_other8.528
r_dihedral_angle_1_deg7.153
r_mcangle_it6.128
r_mcangle_other6.128
r_scangle_it5.765
r_scangle_other5.764
r_mcbond_other3.957
r_mcbond_it3.956
r_scbond_it3.614
r_scbond_other3.613
r_angle_refined_deg1.529
r_angle_other_deg1.195
r_nbd_refined0.214
r_nbd_other0.189
r_symmetry_nbd_other0.179
r_symmetry_xyhbond_nbd_refined0.179
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.128
r_chiral_restr_other0.125
r_symmetry_nbd_refined0.122
r_symmetry_nbtor_other0.078
r_ncsr_local_group_10.074
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3958
Nucleic Acid Atoms
Solvent Atoms64
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
SADABSdata reduction
Aimlessdata scaling
MOLREPphasing